Publications
For most up to date list, see my Google Scholar profile.
Journal Articles
Ponce‐Bobadilla, A. V., Bräm, D., Farnoud, A., Fröhlich, H., Janssen, A., Korsbo, N., et al. (2025). Predictive AI in Clinical Pharmacology: A Call to Action to Develop Robust Benchmarking Practices. CPT: Pharmacometrics & Systems Pharmacology. [Journal]
Bachhav, S. S., Ponce‐Bobadilla, A. V., Clausznitzer, D., Stodtmann, S., & Xiong, H. (2025). Use of Model‐Based Meta‐Analysis to Inform the Design of Early Clinical Trials of Anti‐Amyloid Beta Therapies in Alzheimer’s Disease. CPT: Pharmacometrics & Systems Pharmacology. [Journal]
Ponce‐Bobadilla, A. V., Schmitt, V., Maier, C. S., Mensing, S., & Stodtmann, S. (2024). Practical guide to SHAP analysis: Explaining supervised machine learning model predictions in drug development. Clinical and translational science, 17(11). [Journal]
Stodtmann, S., Chen, M. J., Ponce‐Bobadilla, A. V., Finney‐Hayward, T. K., Kalabic, J., & Mostafa, N. M. SERENE ER Analysis Part 2 SERENE‐UC: Exposure‐response Analysis of Higher Versus Standard Adalimumab Dosing Regimens for Patients with Moderately to Severely Active Ulcerative Colitis. Clinical Pharmacology in Drug Development.[Journal]
Chen, M. J., Ponce‐Bobadilla, A. V., Stodtmann, S., Song, A. P., Finney‐Hayward, T. K., & Mostafa, N. M. (2024). SERENE ER Analysis Part 1‐SERENE CD: Exposure‐Response Analysis of Higher Versus Standard Adalimumab Dosing Regimens for Patients With Moderately to Severely Active Crohn Disease. Clinical Pharmacology in Drug Development.[Journal]
Valderrama, D., Ponce‐Bobadilla, A. V., Mensing, S., Fröhlich, H., & Stodtmann, S. (2024). Integrating machine learning with pharmacokinetic models: Benefits of scientific machine learning in adding neural networks components to existing PK models. CPT: Pharmacometrics & Systems Pharmacology, 13(1), 41-53. [Journal]
Ponce-Bobadilla, A. V., Stodtmann, S., Chen, M. J., Winzenborg, I., Mensing, S., Blaes, J., Haslberger, T., Laplanche, L., Dreher, I. & Mostafa, N. M. (2023). Assessing the Impact of Immunogenicity and Improving Prediction of Trough Concentrations: Population Pharmacokinetic Modeling of Adalimumab in Patients with Crohn’s Disease and Ulcerative Colitis. Clinical Pharmacokinetics, 1-12. [Journal]
Ponce-Bobadilla, A. V., Stodtmann, S., Eckert, D., Zhou, W., Liu, W., & Mohamed, M. E. F. (2023). Upadacitinib Population Pharmacokinetics and Exposure-Response Relationships in Ulcerative Colitis Patients. Clinical Pharmacokinetics, 62(1), 101-112. [Journal]
Ponce-Bobadilla, A.V., Carraro, T., Byrne, H. M., Maini, P. K., Alarcón, T. (2019) Age Structure Can Account for Delayed Logistic Proliferation of Scratch Assays. Bulletin of Mathematical Biology 8(7), p. 2706–2724, doi: 10.1007/s11538-019-00625-w [Preprint] [Journal]
Ponce-Bobadilla, A. V., Arévalo, J., Sarró, E., Byrne, H. M., Maini, P. K., Carraro, T., Balocco, S. & Alarcón, T. (2019). In vitro cell migration quantification method for scratch assays. Journal of the Royal Society Interface. 16, 20180709, doi: 10.1098/rsif.2018.0709. [Preprint] [Journal] [Source code and GUI]
Ponce-Bobadilla, A. V., Maini, P. K., & Byrne, H. M. (2017). A stochastic model for tumour control probability that accounts for repair from sublethal damage. Mathematical Medicine and Biology: A Journal of the IMA. 35(2), p. 181-202. [Journal]
Peer-reviewed Conference Articles
Ponce-Bobadilla, A.V., Bartmanski, B. J., Grima, R., Othmer, H. (2019) The status of the QSSA approximation in stochastic simulations of reaction networks. 2018 Matrix Annals. [Journal]
Ponce-Bobadilla, A. V., Doursat, R., & Amblard, F. (2015). An agent-based model of avascular tumor growth. Proceedings of the European Conference on Artificial Life 2015 (ECAL 2015) University of York, UK, pp. 648-655. [Journal]
Preprints
Song, C., Roller, J., Ponce-Bobadilla, A. V., Palacio-Escat, N., Saez-Rodriguez, J., & Heuveline, V. (2021). Spatial Effect on Separatrix of Two-Cell System and Parameter Sensitivity Analysis. Preprint Series of the Engineering Mathematics and Computing Lab, (01). [Preprint]
Carraro, T., Wetterauer, S. E., Ponce-Bobadilla, A. V., & Trucu, D. (2018). A level-set approach for a multi-scale cancer invasion model, arXiv:1805.07485. [Preprint]
Thesis
PhD thesis: Ponce-Bobadilla, A. V. (2019) Mathematical Models of Cell Migration and Proliferation in Scratch Assays. Heidelberg University, Germany. DOI: 10.11588/heidok.00027466 [Full text]
- MSc thesis 1: Ponce-Bobadilla, A. V. (2015) Stochastic model for tumor control probability: effects of repair from sublethal damage. École Polytechnique, France. [Full text]
- Thesis developed at the Wolfson Centre for Mathematical Biology, University of Oxford, United Kingdom.
- MSc thesis 2: Ponce-Bobadilla, A. V. (2014) Modelling Calcium Waves in Different Dendritic Structures. University of Warwick, United Kingdom. [Full text]